Timeline



Oct 31, 2008:

11:00 AM Changeset [4622] by Nicklas Nordborg
Fixes #1162: Raw bioassay importer fails with …
11:00 AM Ticket #1162 (Raw bioassay importer fails with InvalidUseOfNullException when raw ...) closed by Nicklas Nordborg
fixed: (In [4622]) Fixes #1162: Raw bioassay importer fails with …
10:57 AM Ticket #1162 (Raw bioassay importer fails with InvalidUseOfNullException when raw ...) created by Nicklas Nordborg
The error message should be an ItemNotFoundException? instead so users …
10:51 AM Changeset [4621] by Nicklas Nordborg
Fixes #1158: Improving plugin autodetection
10:51 AM Ticket #1158 (Improving plugin autodetection) closed by Nicklas Nordborg
fixed: (In [4621]) Fixes #1158: Improving plugin autodetection
9:54 AM Ticket #394 (Make it possible to export and properly query values in components) closed by Nicklas Nordborg
fixed: (In [4620]) Fixes #394: Make it possible to export and properly query …
9:54 AM Changeset [4620] by Nicklas Nordborg
Fixes #394: Make it possible to export and properly query values in …

Oct 30, 2008:

2:35 PM Changeset [4619] by Nicklas Nordborg
References #1129: Filtering of child/parent items in table listing …
11:41 AM Changeset [4618] by Nicklas Nordborg
Fixes #1161: Improve error handling in the extension system
11:41 AM Ticket #1161 (Improve error handling in the extension system) closed by Nicklas Nordborg
fixed: (In [4618]) Fixes #1161: Improve error handling in the extension system
8:19 AM Ticket #1149 (Mark related items for removal when "parent" item is marked for removal) closed by Martin Svensson
fixed: (In [4617]) Fixes #1149 Mark related items for removal when "parent" …
8:19 AM Changeset [4617] by Martin Svensson
Fixes #1149 Mark related items for removal when "parent" item is …

Oct 29, 2008:

12:11 PM Ticket #1161 (Improve error handling in the extension system) created by Nicklas Nordborg
The problem is that while an extension may be successfully installed …
11:21 AM Changeset [4616] by Jari Häkkinen
Typo
9:59 AM Changeset [4615] by Nicklas Nordborg
References #1159: Annotation importer should detect non-existing …
9:58 AM Changeset [4614] by Nicklas Nordborg
Fixes #1159: Annotation importer should detect non-existing column mappings
9:58 AM Ticket #1159 (Annotation importer should detect non-existing column mappings) closed by Nicklas Nordborg
fixed: (In [4614]) Fixes #1159: Annotation importer should detect …
9:23 AM Ticket #1129 (Filtering of child/parent items in table listing) closed by Nicklas Nordborg
fixed: (In [4613]) Fixes #1129: Filtering of child/parent items in table …
9:23 AM Changeset [4613] by Nicklas Nordborg
Fixes #1129: Filtering of child/parent items in table listing …

Oct 28, 2008:

4:41 PM Changeset [4612] by Martin Svensson
References #1149 Items that are linked to from a transformation are …
3:00 PM Ticket #1160 (MeV export: Base1 style column headers should be changed to BASE 2 style) created by Jari Häkkinen
The three first column headers in MeV export uses Base1 names. These …
2:50 PM Changeset [4611] by Nicklas Nordborg
References #1092: Add listing of child items that are the same type as …
2:20 PM Changeset [4610] by Nicklas Nordborg
References #1129: Filtering of child/parent items in table listing …
1:22 PM Changeset [4609] by Nicklas Nordborg
References #1129: Filtering of child/parent items in table listing …
1:20 PM Changeset [4608] by Nicklas Nordborg
References #792: Add support for units to annotation values Fixes …
9:16 AM Changeset [4607] by Nicklas Nordborg
References #1129: Filtering of child/parent items in table listing …

Oct 27, 2008:

4:20 PM Changeset [4606] by Martin Svensson
Fixes #1152 Improve transaction handling in Base1PluginExecuter. There …
4:20 PM Ticket #1152 (Improve transaction handling in Base1PluginExecuter) closed by Martin Svensson
fixed: (In [4606]) Fixes #1152 Improve transaction handling in …
10:00 AM Changeset [4605] by Nicklas Nordborg
Merged patch release 2.8.4 to the trunk
9:45 AM Milestone BASE 2.8.4 completed
Bug fixes for 2.8.3. Revision Log: log:branches/2.8-stable@4583:4603
9:45 AM DownloadPage edited by Nicklas Nordborg
Releasing 2.8.4 (diff)
9:41 AM Changeset [4604] by Nicklas Nordborg
Changes for future release 2.8.5
9:24 AM Changeset [4603] by Nicklas Nordborg
Tagging version 2.8.4
9:23 AM Changeset [4602] by Nicklas Nordborg
Preparing release 2.8.4
9:06 AM Ticket #1159 (Annotation importer should detect non-existing column mappings) created by Nicklas Nordborg
The detection should be done in the job configuration phase and …
9:02 AM Ticket #1157 (Annotation importer fails with NullPointerException in end()) closed by Nicklas Nordborg
fixed: (In [4601]) Fixes #1157: Annotation importer fails with …
9:02 AM Changeset [4601] by Nicklas Nordborg
Fixes #1157: Annotation importer fails with NullPointerException? in end()
8:30 AM Ticket #1157 (Annotation importer fails with NullPointerException in end()) reopened by Nicklas Nordborg
Hmmm... I can't see how a missing Data footer in the file can lead to …

Oct 24, 2008:

4:22 PM Ticket #1157 (Annotation importer fails with NullPointerException in end()) closed by Jari Häkkinen
invalid: After getting more details about this I realize that there was a 'Data …
1:43 PM Changeset [4600] by Nicklas Nordborg
Fixes #1156: Add support for ALL and ANY constructs to the Query API
1:43 PM Ticket #1156 (Add support for ALL and ANY constructs to the Query API) closed by Nicklas Nordborg
fixed: (In [4600]) Fixes #1156: Add support for ALL and ANY constructs to the …
8:39 AM Changeset [4599] by Nicklas Nordborg
References #1157: Removed last empty line to check if this breaks the …

Oct 23, 2008:

10:28 PM Ticket #1158 (Improving plugin autodetection) created by Jari Häkkinen
The auto detection of plug-ins can be improved. As it is now starting …
4:16 PM Ticket #1157 (Annotation importer fails with NullPointerException in end()) created by Jari Häkkinen
The number of columns is correct. After adding the new line in the …
12:38 PM Ticket #1156 (Add support for ALL and ANY constructs to the Query API) created by Nicklas Nordborg
This is needed for solving #1129. It would allow create queries like …

Oct 22, 2008:

1:41 PM Changeset [4598] by Nicklas Nordborg
References #1145: Make the generic raw data importer support batch …
1:07 PM Ticket #1155 (Automatic plug-in registration wizard should group plug-ins by JAR file) created by Nicklas Nordborg
When there are many plug-in JAR files in the base.plugins directory …
1:00 PM Ticket #1154 (Add a 'Plug-in package' item for grouping plug-ins) created by Nicklas Nordborg
The plug-in administration page contains more and more plug-ins. It …
11:46 AM Changeset [4597] by Martin Svensson
Fixes #1142 Lack of permission when trying to write to an item or use …
11:46 AM Ticket #1142 (Batch importer plug-ins should handle lack of USE permission better) closed by Martin Svensson
fixed: (In [4597]) Fixes #1142 Lack of permission when trying to write to an …
10:43 AM Ticket #1153 (Handling short read transcript sequence data) created by base
This may not be a "core" issue, it might be achieved with core or …
9:19 AM Changeset [4596] by Nicklas Nordborg
References #792: Add support for units to annotation values Fixes a …

Oct 21, 2008:

11:33 AM Ticket #1142 (Batch importer plug-ins should handle lack of USE permission better) reopened by Martin Svensson
There are two more cases where the permission handling can be improved.
9:44 AM Changeset [4595] by Martin Svensson
Fixes #1142 Batch importer plug-ins should handle lack of USE …
9:44 AM Ticket #1142 (Batch importer plug-ins should handle lack of USE permission better) closed by Martin Svensson
fixed: (In [4595]) Fixes #1142 Batch importer plug-ins should handle lack of …
9:20 AM Changeset [4594] by Nicklas Nordborg
Fixes #1145: Make the generic raw data importer support batch import
9:20 AM Ticket #1145 (Make the generic raw data importer support batch import) closed by Nicklas Nordborg
fixed: (In [4594]) Fixes #1145: Make the generic raw data importer support …
8:56 AM Ticket #1152 (Improve transaction handling in Base1PluginExecuter) created by Nicklas Nordborg
The Base1PluginExecuter currently opens and closes transactions in …
8:47 AM Changeset [4593] by Nicklas Nordborg
Fixes #1150: Incorrect mapping of BASE1/BASE2 differences by …
8:47 AM Ticket #1150 (Incorrect mapping of BASE1/BASE2 differences by Base1PluginExecuter) closed by Nicklas Nordborg
fixed: (In [4593]) Fixes #1150: Incorrect mapping of BASE1/BASE2 differences …

Oct 20, 2008:

12:58 PM Ticket #1151 (Create a batch-importer version of the 'roles' test procedure) created by Nicklas Nordborg
The 'roles' test program is already 1. A manual test procedure to …
11:08 AM Changeset [4592] by Nicklas Nordborg
References #1150: Incorrect mapping of BASE1/BASE2 differences by …
9:08 AM Changeset [4591] by Nicklas Nordborg
Fixes #1147: Incorrect result from isUsed() method prevents deletion …
9:08 AM Ticket #1147 (Incorrect result from isUsed() method prevents deletion of some items) closed by Nicklas Nordborg
fixed: (In [4591]) Fixes #1147: Incorrect result from isUsed() method …

Oct 17, 2008:

9:18 AM Ticket #1150 (Incorrect mapping of BASE1/BASE2 differences by Base1PluginExecuter) created by Nicklas Nordborg
As an example if a BASE1-plugin asks for 'geneSymbol' the generated …

Oct 16, 2008:

10:06 PM Ticket #1149 (Mark related items for removal when "parent" item is marked for removal) created by Jari Häkkinen
When a transformation is deleted in the analysis view the created …
9:57 PM Ticket #1148 (Removing items from trashcan when circular references exists ...) created by Jari Häkkinen
is probably not easy. However, when an item is blocked by another item …
9:48 PM Ticket #1147 (Incorrect result from isUsed() method prevents deletion of some items) created by Jari Häkkinen
The trashcan view shows the dependency icon for the item but clicking …
9:26 PM Changeset [4590] by Jari Häkkinen
Fixed typo.
1:23 PM Ticket #1146 (updateindexes.sh should create indexes for foreign keys) closed by Nicklas Nordborg
fixed: (In [4589]) Fixes #1146: updateindexes.sh should create indexes for …
1:23 PM Changeset [4589] by Nicklas Nordborg
Fixes #1146: updateindexes.sh should create indexes for foreign keys
12:13 PM Changeset [4588] by Martin Svensson
Fixes #1136 Give away/set owner of items
12:13 PM Ticket #1136 (Give away/set owner of items) closed by Martin Svensson
fixed: (In [4588]) Fixes #1136 Give away/set owner of items
11:25 AM Ticket #1146 (updateindexes.sh should create indexes for foreign keys) created by Nicklas Nordborg
MySQL automatically generates an index on all foreign key columns, but …
8:31 AM Ticket #1145 (Make the generic raw data importer support batch import) created by Nicklas Nordborg
This ticket replaces #1135. The multi-import feature should be …

Oct 15, 2008:

4:40 PM Changeset [4587] by Martin Svensson
References #1136 Change to fit all jsp-pages, including files, and …
3:14 PM Changeset [4586] by Nicklas Nordborg
This directory was added in [4574] by accident.
3:13 PM Changeset [4585] by Nicklas Nordborg
Merged patch release 2.8.3 to the trunk.
2:10 PM Milestone BASE 2.8.3 completed
Revision Log: log:branches/2.8-stable@4535:4583
2:10 PM DownloadPage edited by Nicklas Nordborg
Releasing BASE 2.8.3 (diff)
2:05 PM Changeset [4584] by Nicklas Nordborg
Changes for future release 2.8.4
1:44 PM Changeset [4583] by Nicklas Nordborg
Tagging version 2.8.3
1:43 PM Changeset [4582] by Nicklas Nordborg
Preparing release 2.8.3
1:41 PM Changeset [4581] by Nicklas Nordborg
Fixes #1144: Test program for Base1PluginExecuter doesn't report a failure
1:41 PM Ticket #1144 (Test program for Base1PluginExecuter doesn't report a failure) closed by Nicklas Nordborg
fixed: (In [4581]) Fixes #1144: Test program for Base1PluginExecuter doesn't …
1:40 PM Ticket #1144 (Test program for Base1PluginExecuter doesn't report a failure) created by Nicklas Nordborg
I was running the test program on Windows which of course fails …
1:34 PM Changeset [4580] by Nicklas Nordborg
References #1131: Permission problems creating a new directory in a …
1:10 PM Ticket #1143 (Problems with file browser and Internet Explorer) closed by Nicklas Nordborg
fixed: I have now verified the fix.

Oct 14, 2008:

9:46 AM Changeset [4579] by Nicklas Nordborg
References #1143: Problems with file browser and Internet Explorer I …
8:59 AM Ticket #1143 (Problems with file browser and Internet Explorer) created by Nicklas Nordborg
We have been experiencing some intermittent and strange problems with …

Oct 13, 2008:

4:38 PM Changeset [4578] by Martin Svensson
References #1136 Updated most of the index-, view- and list-jsp pages …
11:38 AM Changeset [4577] by Nicklas Nordborg
References #792: Add support for units to annotation values Make it …
11:04 AM Ticket #1122 (News item sort order should be controllable) closed by Nicklas Nordborg
fixed: (In [4576]) Fixes #1122: News item sort order should be controllable
11:04 AM Changeset [4576] by Nicklas Nordborg
Fixes #1122: News item sort order should be controllable
10:57 AM Changeset [4575] by Nicklas Nordborg
Fixes #1121: News item 'BASE Server installed' is created after …
10:57 AM Ticket #1121 (News item 'BASE Server installed' is created after running updatedb) closed by Nicklas Nordborg
fixed: (In [4575]) Fixes #1121: News item 'BASE Server installed' is created …
9:52 AM Ticket #1142 (Batch importer plug-ins should handle lack of USE permission better) created by Nicklas Nordborg
The current implementation of the batch importer simply ignores all …
9:43 AM Changeset [4574] by Nicklas Nordborg
Fixes #1137: Importing hybridizations fail when association is tried …
9:43 AM Ticket #1137 (Importing hybridizations fail when association is tried to a slide ...) closed by Nicklas Nordborg
fixed: (In [4574]) Fixes #1137: Importing hybridizations fail when …

Oct 10, 2008:

4:37 PM Changeset [4573] by Martin Svensson
References #1136 Added ownership-jsppages and also started to updated …
12:17 PM Ticket #1138 (SMART option for feature mismatch in rawbioassay import does not work) closed by Nicklas Nordborg
invalid: It is more or less impossible to delete the entries since there are …

Oct 9, 2008:

2:56 PM Ticket #1141 (Spelling error for "Disk usage") closed by Nicklas Nordborg
fixed: (In [4572]) Fixes #1141: Spelling error for "Disk usage"
2:56 PM Changeset [4572] by Nicklas Nordborg
Fixes #1141: Spelling error for "Disk usage"
2:47 PM Ticket #1141 (Spelling error for "Disk usage") created by Nicklas Nordborg
It is spelled "Disc usage" in several places, for example in the role …
2:36 PM Changeset [4571] by Nicklas Nordborg
Fixes #1140: Unclosed DbControl?
2:36 PM Ticket #1140 (Unclosed dbcontrol) closed by Nicklas Nordborg
fixed: (In [4571]) Fixes #1140: Unclosed DbControl?
12:40 PM Ticket #1140 (Unclosed dbcontrol) created by Martin Svensson
[…]
10:00 AM Ticket #1139 (Display the barcode for array slide in the hybridization information page) created by Jari Häkkinen
Currently the slide name is displayed on the hybridization information …
9:56 AM Ticket #1138 (SMART option for feature mismatch in rawbioassay import does not work) created by Jari Häkkinen
We have problems with the SMART option for feature mismatch error …
9:23 AM Ticket #1137 (Importing hybridizations fail when association is tried to a slide ...) created by Jari Häkkinen
Hybs and slides have a 1-to-1 relation so the problem is expected. …

Oct 8, 2008:

2:35 PM Ticket #1125 (Replace existing file in file upload) closed by Martin Svensson
fixed: (In [4570]) Fixes #1125 Replace existing file in file upload
2:35 PM Changeset [4570] by Martin Svensson
Fixes #1125 Replace existing file in file upload
10:20 AM Ticket #1136 (Give away/set owner of items) created by Jari Häkkinen
In ticket:348 take ownership was added to BASE, why is set ownership …
9:18 AM Changeset [4569] by Nicklas Nordborg
Fixes #1134: Raw bioassays are available for inclusion in root …
9:18 AM Ticket #1134 (Raw bioassays are available for inclusion in root bioassay creation ...) closed by Nicklas Nordborg
fixed: (In [4569]) Fixes #1134: Raw bioassays are available for inclusion in …

Oct 7, 2008:

3:54 PM Changeset [4568] by Martin Svensson
Fixes #1105 Automatically set "array design" on raw bioassay that has …
3:54 PM Ticket #1105 (Automatically set "array design" on raw bioassay that has link via ...) closed by Martin Svensson
fixed: (In [4568]) Fixes #1105 Automatically set "array design" on raw …
2:18 PM Ticket #1135 (Create plug-in for importing raw data to multiple raw bioassays in one go) created by Jari Häkkinen
The batch importers now support creation of items down to RawBioAssay …
2:13 PM Changeset [4567] by Nicklas Nordborg
Fixes #1113 and #1114: "Broadcast to currently active BASE users" and …
2:13 PM Tickets #1113,​1114 batch updated by Nicklas Nordborg
fixed: (In [4567]) Fixes #1113 and #1114: "Broadcast to currently active BASE …
1:50 PM Ticket #1134 (Raw bioassays are available for inclusion in root bioassay creation ...) created by Jari Häkkinen
Creating a new root bioassay from raw bioassays in some cases fail …
11:37 AM Changeset [4566] by Nicklas Nordborg
References #792: Add support for units to annotation values Added …
10:44 AM Ticket #1133 (Experimental factors - inherit annotations) created by base
I have in BASE2 created a new annotation at the Biosource level. When …
9:58 AM Changeset [4565] by Nicklas Nordborg
References #792: Add support for units to annotation values Added …
9:57 AM Ticket #1104 (Automatically set "number of arrays" on hybridization that has link to ...) closed by Martin Svensson
fixed: (In [4564]) Fixes #1104 Automatically set "number of arrays" on …
9:57 AM Changeset [4564] by Martin Svensson
Fixes #1104 Automatically set "number of arrays" on hybridization that …
9:12 AM Changeset [4563] by Martin Svensson
References #1104, Updating the 'number of arrays'-field when an …

Oct 6, 2008:

2:10 PM Changeset [4562] by Nicklas Nordborg
References #792: Add support for units to annotation values Added …
11:18 AM Changeset [4561] by Nicklas Nordborg
References #792: Add support for units to annotation values Updated …
11:14 AM WikiStart edited by Nicklas Nordborg
Removed links to trunk versions since there is no published trunk … (diff)
9:27 AM DeveloperInformation edited by Nicklas Nordborg
Removed links to trunk versions since there is no published trunk … (diff)
9:22 AM Changeset [4560] by Nicklas Nordborg
References #792: Add support for units to annotation values All list …

Oct 3, 2008:

4:23 PM Changeset [4559] by Martin Svensson
Fixes #1092 Add listing of child items that are the same type as the parent
4:23 PM Ticket #1092 (Add listing of child items that are the same type as the parent) closed by Martin Svensson
fixed: (In [4559]) Fixes #1092 Add listing of child items that are the same …
2:26 PM Changeset [4558] by Nicklas Nordborg
References #792: Add support for units to annotation values Added …
12:28 PM Changeset [4557] by Nicklas Nordborg
References #792: Add support for units to annotation values Made …
10:56 AM Changeset [4556] by Nicklas Nordborg
References #792: Add support for units to annotation values …

Oct 2, 2008:

1:55 PM Changeset [4555] by Nicklas Nordborg
References #792: Add support for units to annotation values Made it …
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